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mammoth insight into antibiotic resistance

It's no secret our great technological and scientific triumphs often reveal unforeseen problems, even as they are being employed to better our lives...

By Erling Friis-Baastad

It’s no secret our great technological and scientific triumphs often reveal unforeseen problems, even as they are being employed to better our lives. Consider nuclear power - clean, readily available and effective - but deadly when combined with human shortcomings, such as greed and haste.

Medicine has recently encountered another such mixed blessing, this time with antibiotics. Some drugs we’ve come to rely on to stop infection are becoming less effective, as the organisms they target “learn” to fight back.

Now, thanks to work undertaken in the Klondike gold fields, scientists are beginning to understand why we are finding ourselves confronted with antibiotic-resistant diseases.

Earth scientist and permafrost expert Duane Froese of the University of Alberta, Edmonton, was a member of an eclectic team of scientists who analyzed data from frozen earth exposed by placer mining on Bear Creek, south of Dawson City. They recently published the results of their labours, “Antibiotic resistance is ancient,” in the journal Nature.

“What this study showed is that some of the resistance elements that we know are problematic in terms of present-day clinical medicine ... are at least 30,000 years old and must predate any human impacts in terms of what’s going on in microbial communities, bacteria and things like that,” says Froese.

By drilling into the frozen microbial “archive” of the Klondike, Froese and fellow scientists, including, among others, McMaster University microbiologists Gerry Wright and Hendrik Poinar, and Yukon paleontologist Grant Zazula, discovered genetic traces of ancient “germ warfare.”

This warfare was essentially that of microbes fighting microbes. Some used antibiotics to kill their competition; in turn, the competition somehow developed antibiotic resistance. “We don’t know quite how they create their strategy or how others create antibiotic resistance but it must help them in terms of this competition,” says Froese. Because antibiotics are essentially synthesized from the soil, we inherit the results of this evolutionary miracle.

Why seek an explanation of a worldwide problem in the Yukon? “The Klondike is really a special place, almost unique in the Northern Hemisphere because you have volcanic ashes interbedded in permafrost and so we can go to frozen materials - permafrost - and know where we are in time,” says Froese, who has been working in the area on and off for about 18 years.

As well, famously co-operative Klondike placer miners allow scientists onto their claims and into excavations they have made down through overburden to reach gold-bearing dirt.

“We picked a site where we knew the age very well,” says Froese. “There’s widespread volcanic ash called Dawson tephra, which is about 30,000 years old, and we were able to take some permafrost samples from immediately below that.”

Permafrost acts as a great deepfreeze, preventing or retarding the breakdown and dissolution of genetic material.

The idea was that because “genetic dandruff,” sedimentary DNA, is constantly sloughing off living things - including animals, plants and people - scientists could find, not only fallout from microbial battles, but clues as to what the environment the microbes fought in looked like. Researchers could identify the flora and fauna that lived on and in the soil the microbes inhabited.

If the genetic materials that are related to antibiotic resistance appear in core samples containing traces of, say, ice-age mammoth DNA, but not traces of today’s boreal creatures such as moose and elk, or modern plants like spruce, then we can get a pretty good idea that the resistance was around at least as far back as the Pleistocene.

Because contaminated data would lead scientists astray when dating their finds, extracting genetic samples from the cores is a very meticulous process, says Froese. The drills used to remove cores from the permafrost, and then the cores themselves are sprayed with a “water mixture with a lab-derived bacteria that includes a fluorescent protein from jelly fish.”

The cores are kept frozen until scientists can drill into them back at the lab. If no fluorescence appears within the cores, researchers can be assured the material has not been contaminated during the extraction and preservation processes. Should pockets of fluorescence appear, the scientists know their cores have been compromised somehow during handling.

The Bear Creek cores proved clean.

The researchers then amplify the DNA found in the core, “making thousands to millions of copies of the DNA” looking for sequences, essentially strings of nucleotides, that are distinctive to particular antibiotic-resistant genes.

The conflict between biotics and antibiotics likely predated 30,000 years, says Froese. “It’s just that the rates of genetic degradation are so slow in permafrost we can go back 30,000 years. We don’t actually have a natural archive on the planet where we can go back millions of years. DNA will degrade over that time.”

For now, it would appear to be sufficient to realize that the backstory to antibiotic resistance extends at least as far back as the last ice age. “There’s a huge reservoir of resistance out there,” says Froese.

“It’s a great diversity ... and can emerge when it has the opportunity.” Such an opportunity has been provided over the past 60 to 70 years as strong evolutionary pressure has been applied by our much-too-heavy use of antibiotics.

The message the researchers brought back to their laboratories from Bear Creek is very simple, he stresses. “You don’t have to know anything about the structure of molecules or any of that kind of stuff to get the gist of it:

“We have to be really careful about the way we use antibiotics.”

This column is co-ordinated by the Northern Research Institute at Yukon College with major financial support from Environment Yukon and Yukon College/ The articles are archived at